Abstract 6639: Optimized selection of tumor-informed MRD panels enhances sensitivity of ctDNA detection

Abstract Circulating tumor DNA (ctDNA) is a highly sensitive and specific biomarker for molecular residual disease (MRD) and can be by identified by the presence of tumor-specific somatic variants. We have developed a second-generation hybrid-capture-based tumor-informed MRD assay to detect the presence and quantity of ctDNA in plasma-derived cell-free DNA (cfDNA). Our assay surveys the whole tumor genome to identify the superset of high-confidence somatic variant targets that can be used to distinguish ctDNA from non-tumor cfDNA. Each panel consists of up to 1000 targets that are selected based on target-specific and tumor-specific features that impact the representation of tumor variants or the effective molecular depth of a panel, such as somatic call confidence, zygosity, copy number, background error rate and expected molecular depth following capture and sequencing. cfDNA captured using a patient-matched panel undergoes targeted sequencing and that sequence data is fit to a statistical model that evaluates the presence and fraction of ctDNA in the sample. Here, we evaluated the performance of our target-ranking algorithm using contrived mixtures of matched tumor and normal cell lines, with tumor DNA concentrations ranging from 5 to 10, 000 parts per million (ppm) and samples processed across multiple days, reagent lots, operators and instruments. Identical sets of contrived samples were analyzed using subsets of panel targets, including top-ranking and bottom-ranking target sets. We found the Limit of Detection with 95% sensitivity (LoD95) for top-ranking targets was 40% of the LoD95 for low-ranking targets, demonstrating the effectiveness of our ranking algorithm in stratifying high and low sensitivity targets. In conclusion, the constituents of tumor-informed MRD panels have a measurable impact on the sensitivity of ctDNA detection and, with optimization, can enhance the resolution of residual disease detection. Citation Format: Ashley Acevedo, Ravi Patel, Kyle Trettin, Nafei Xu, Genevieve Gould, Dale Muzzey. Optimized selection of tumor-informed MRD panels enhances sensitivity of ctDNA detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6639.